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A man faces numerous charges after two missing children — one of whom was the subject of an Amber Alert — were found in Orange County last week following a manhunt that spanned multiple states, officials said Monday.

Jacob Francis Allen Clare, 35, was charged with one count of kidnapping, two counts of unlawful sexual intercourse with a minor, two counts of oral copulation with a minor, a count of sexual penetration by a foreign object of a minor and two counts of incest, according to the Orange County District Attorney’s Office.

Clare is accused of kidnapping his 3-year-old son, who was supposed to be returned to his mother after a scheduled visit, more than two weeks ago, prosecutors say. The toddler’s mother reported the pair missing out of Tennessee on Nov. 7.

A few days later, the suspect’s teenage niece, who lives in Kentucky, was also reported missing from her home, according to investigators. They believe she went willingly with her uncle as he took both kids across the country to Southern California.

An Amber Alert was issued by the Tennessee Bureau of Investigations in regards to the missing boy, and authorities identified his father as the suspect. That triggered a multi-state search for the trio.

Last Tuesday, Clare’s abandoned vehicle was located in San Clemente, which prompted the California Highway Patrol to issue an endangered missing advisory for the children in five Southland counties.

Two days later, a good Samaritan spotted the missing children in Dana Point and alerted the Orange County Sheriff’s Department. Her tip led to the recovery of the children and the arrest of the suspect, according to law enforcement.

The kids have since been reunited with their mothers.

Prosecutors allege Clare sexually assaulted his niece between Nov. 11 and 18.

“The blatant exploitation of these children and the pain and misery the actions of a single individual has caused is unconscionable. These are innocent children and the selfish and depraved acts of this individual ripped a little boy out of the arms of his mother and stole the innocence of a little girl,” DA Todd Spitzer said. “The Orange County District Attorney’s Office will do everything it can to prevent this monster from hurting any more children.”

If convicted as charged, Clare faces a maximum prison sentence of 14 years. He also faces other charges back in Tennessee, according to prosecutors.

The defendant is expected to be arraigned Monday. He’s being held without bail.